Report generated on 2019-10-27, 12:13 based on data in:
/mnt/research/ShadeLab/GLBRC/mapping/metaG/fullAssembly/trimStats
Trimmomatic is a flexible read trimming tool for Illumina NGS data.
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from IPython.core.display import HTML

Method: Reads were trimmed, aligned to the host assembly, and reads with neither pair aligninging were extracted and aligned to the collection of fungal assemblies. All reads with neither pair aligned to the fungal assemblies were extracted again in "cleaned" fastq files. MegaHit was then used with the "--kmin-1pass" and "--presets meta-large" options to generate a metagenomic assembly.
Step 1. Split JGI files in PE files
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# <!-- # #HIDDEN
# # tImages = {"MetaG":Image("images/TrimReport_MetaG.png"),"MetaT":Image("images/MetaT_trimmomatic_plot.png")}
# # @interact
# # def trimReport(Source=["MetaG","MetaT"]):return tImages[Source]
# <img src="images/TrimReport_MetaG.png"></img>
# -->
HTML("html/MetaG_TrimStats.html")
Step 1. Align reads to respective host reference assembly
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HTML(filename="html/BothPerc.html")
Step 1. Extract reads that don't align the plant assembly
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HTML(filename='html/FungalAlign.html')
Method: Reads were trimmed, aligned to the host assembly, and reads with neither pair aligninging were extracted and aligned to the collection of fungal assemblies. All reads with neither pair aligned to the fungal assemblies were extracted again in "cleaned" fastq files. MegaHit was then used with the "--kmin-1pass" and "--presets meta-large" options to generate a metagenomic assembly.
The annotations were performed using KEGG's prokaryotic peptides and eukaryotic peptides

Based on the high-overlap, we decided to use the mags instead of the assembly for alignment
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HTML(filename="html/MAG_Stats.html")
MetaG Analysis¶
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Call: adonis(formula = dist.otu ~ map_16S\$time_numeric)
Permutation: free Number of permutations: 999
Terms added sequentially (first to last)
| Df | SumsOfSqs | MeanSqs | F.Model | R2 | Pr(>F) | |
|---|---|---|---|---|---|---|
| map_16S$time_numeric | 1 | 1.9356 | 1.93562 | 47.814 | 0.26298 | 0.001 *** |
| Residuals | 134 | 5.4246 | 0.04048 | 0.73702 | ||
| Total | 135 | 7.3603 | 1.000000 |


Call: adonis(formula = dist.otu ~ map_16S\$treatment)
Permutation: free Number of permutations: 999
Terms added sequentially (first to last)
| Df | SumsOfSqs | MeanSqs | F.Model | R2 | Pr(>F) | |
|---|---|---|---|---|---|---|
| map_16S$treatment | 1 | 0.0289 | 0.028930 | 0.52878 | 0.00393 | 0.755 |
| Residuals | 134 | 7.3313 | 0.054711 | 0.99607 | ||
| Total | 135 | 7.3603 | 1.000000 |
Call: adonis(formula = dist.otu ~ map_16S\$plant)
Permutation: free Number of permutations: 999
Terms added sequentially (first to last)
| Df | SumsOfSqs | MeanSqs | F.Model | R2 | Pr(>F) | |
|---|---|---|---|---|---|---|
| map_16S$plant | 1 | 0.1617 | 0.161704 | 3.0101 | 0.02197 | 0.027 * |
| Residuals | 134 | 7.1986 | 0.053721 | 0.97803 | ||
| Total | 135 | 7.3603 | 1.000000 |
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